rs2021808

Positions:

• chr7-128229638-G-A
• chr7-128229638-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000692614.2(ENSG00000289434):​n.519+6620C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,278 control chromosomes in the GnomAD database, including 52,663 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.81 (52663 hom., cov: 34)
• Consequence: ENST00000692614.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692614.2	n.519+6620C>T		intron_variant, non_coding_transcript_variant
	ENST00000690022.1	n.243+6620C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122943 AN: 152162 Hom.: 52637 Cov.: 34

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.838

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.808 AC: 123020 AN: 152278 Hom.: 52663 Cov.: 34 AF XY: 0.813 AC XY: 60566 AN XY: 74474

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.941

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.932

Gnomad4 OTH AF: 0.839

Alfa AF: 0.916 Hom.: 83037

Bravo AF: 0.792

Asia WGS AF: 0.907 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.37
DANN	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2021808; hg19: chr7-127869691;